Github code
Scientific Question: Given the significant reduction for the risk of breast cancer after obese patients undergo bariatric surgery, what specific genes are responsible for the reduced risk and how do the expression levels of these certain genes change after the surgery?
Hypothesis: If the levels of Estrogen Receptor Alpha decrease after bariatric surgery, then by analyzing the specific gene (ESR1) expression levels of this protein and associated pathways will show a marked change from pre-weight loss surgery levels that are responsible for the preventative phenotype against breast cancer.
The packages Edger and limma are used to filter out lowly expressed counts and to model the voom plot in RNA-seq and also EdgeR is used in Pathway analysis to gain access to cerrtain functions
library(edgeR)
library(limma)The package msa used to align multiple sequences from a single fasta file with its function msa
library(msa)seqdata<- read.csv("/Users/heatherotto/Downloads/GSE126803_AI007_Readcounts.csv")
seqdatadim(seqdata)[1] 19645 61countdata<- seqdata[,-(1)]
countdatarownames(countdata) <- seqdata[,1]
head(countdata)sampleinfo<- read.delim("/Users/heatherotto/Sampleinfo copy.txt", row.names= NULL)colnames(sampleinfo) <- colnames(sampleinfo)[2:ncol(sampleinfo)]
sampleinfosampleinfo<- sampleinfo[, -(3:4)]
sampleinfoy<- DGEList(countdata)
yAn object of class "DGEList"
$counts
AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B 0.08969942 0.1377730 0.4689322 0.6425727 0.2710652 0.2390679
CLASP1 8.29223807 6.9066242 10.0749860 9.0827100 12.9326915 8.8306438
TSC2 20.41821708 20.9614251 14.6790392 21.8024361 22.7280129 17.6134194
ERGIC2 24.29453789 31.6844127 36.8340772 33.1361719 33.7938411 34.6500575
SPG20OS 0.51340170 0.4293197 0.0000000 0.0677277 0.8594560 0.3434817
AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B 0.3810158 0.02985079 0.3991934 0.04679104 0.000000 0.1567836
CLASP1 8.5018542 7.41074318 9.2111196 8.82339225 8.252884 8.5378324
TSC2 20.5334382 22.90115266 17.9478907 27.03462975 18.732465 16.9429477
ERGIC2 28.0519829 19.67938260 25.6030502 25.31411789 27.274788 31.6587906
SPG20OS 0.3375794 0.65612606 0.4714289 0.38284594 0.000000 0.3943235
AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B 0.0501999 0.09899953 0.06860305 0.1752291 0.09320857 0.04430422
CLASP1 8.8948742 11.14349889 9.53456943 9.2975701 8.20042424 8.39604851
TSC2 22.7482431 18.68817115 14.17456014 21.7803833 16.24760807 16.16759857
ERGIC2 27.6848779 25.12473641 33.27308743 40.7538765 29.55974952 29.14257278
SPG20OS 0.7444397 0.32698846 0.08126292 0.0000000 0.15388827 0.35194182
AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B 0.3536386 0.1603581 0.02380131 0.09098328 0.13393686 0.06969021 0.03364489
CLASP1 9.6874216 11.2414363 4.81093742 8.95276389 9.40307322 8.58215847 6.31334240
TSC2 16.2564699 16.5288894 11.98917274 18.41631154 21.51137553 15.50351101 15.23328212
ERGIC2 34.8356066 36.1047479 17.25532438 31.16564676 38.77159560 34.22509806 36.16802991
SPG20OS 1.1519228 0.1827098 0.37986174 0.05784366 0.05784366 0.42124056 0.28019428
AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B 0.4911890 0.3610493 0.1136028 0.09291356 0.01116544 0.00000 0.05779537
CLASP1 8.8250530 11.4324839 8.2329628 7.89373506 11.08134880 12.52725 10.05180875
TSC2 14.4110359 19.3913762 19.0121881 19.86529843 19.42022476 23.86788 25.82734610
ERGIC2 40.6769330 16.2188413 32.0814595 36.98349010 28.48121922 24.21277 27.16994391
SPG20OS 0.4795911 0.1835943 0.3755042 0.05213495 1.56143639 0.00000 0.29807249
AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B 0.19430432 0.2393998 0.1357762 0.06355554 0.02536228 0.1194512 0.1759087
CLASP1 12.04448929 8.6591094 8.3761595 9.35402683 5.99278228 9.2258454 8.6915694
TSC2 14.85757132 15.4644994 14.3929859 22.85739826 32.78989079 16.0272630 23.8790380
ERGIC2 31.08928686 36.3008713 27.5867316 52.14664520 15.80894345 33.7884990 25.5698107
SPG20OS 0.09558827 0.1267672 0.0000000 0.39923433 0.30728566 0.0000000 1.2991460
AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B 0.03254789 0.07536732 0.1879747 0.07500112 0.23588178 0.22121742 0.24536749
CLASP1 8.59145698 8.92918670 10.2306575 7.69298607 4.63658607 10.72337215 8.79752802
TSC2 19.74323945 20.30813567 19.6965824 17.38359714 28.39474488 20.30840905 15.84455339
ERGIC2 24.17770466 31.09084848 35.7840620 23.88359358 9.94057162 21.77228556 34.61117909
SPG20OS 0.06013589 0.09353621 0.1749615 0.09183099 0.08263845 0.07534792 0.07605192
AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B 0.03151935 0.02822746 0.2077901 0.09047029 9.650265e-04 0.3415222 0.2326068
CLASP1 11.58481344 10.31491832 9.7284928 9.38149203 7.210589e+00 11.0368002 6.2912171
TSC2 18.91443947 16.63015918 19.3889038 17.18876511 1.596532e+01 14.3247503 27.8789860
ERGIC2 25.76242226 33.89741809 29.5176014 31.56035801 2.612456e+01 30.6970516 18.1402925
SPG20OS 0.80623522 0.34338226 0.4916952 0.80873645 5.784366e-02 0.2776951 0.1834748
AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B 0.36919153 0.1681029 0.05386508 0.01116544 0.16008039 0.2963357 0.01116544
CLASP1 11.24710885 8.8419275 12.24037933 11.55106685 8.44684402 6.7596874 8.82584809
TSC2 22.02743093 22.4983255 14.26515557 28.16410194 18.75746435 23.1045227 17.81352521
ERGIC2 26.32010071 29.1152262 35.10153190 31.64211155 35.30127013 23.5141753 28.86583911
SPG20OS 0.05784366 0.1847546 0.19649589 0.47239067 0.05213495 0.4902792 0.05213495
19640 more rows ...
$samples55 more rows ...group<- paste(sampleinfo$Surgery.Status, sep= ".")
group [1] " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s"
[10] " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s"
[19] " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s" " post.s"
[28] " post.s" " post.s" " post.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s"
[37] " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s"
[46] " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s"
[55] " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" " pre.s" group<- factor(group)
group [1] post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s
[13] post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s post.s
[25] post.s post.s post.s post.s post.s post.s pre.s pre.s pre.s pre.s pre.s pre.s
[37] pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s
[49] pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s pre.s
Levels: post.s pre.sy$samples$group<- group
y$samplesCPM<- cpm(countdata)
head(CPM) AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B 0.1376810 0.184955 0.7766311 1.0253981 0.4459015 0.3555442
CLASP1 12.7278790 9.271876 16.6858846 14.4939145 21.2742457 13.1330206
TSC2 31.3402237 28.139903 24.3109770 34.7916695 37.3875254 26.1948512
ERGIC2 37.2900458 42.535099 61.0034754 52.8777032 55.5907855 51.5319075
SPG20OS 0.7880279 0.576345 0.0000000 0.1080778 1.4138030 0.5108293
HLX 9.9572347 9.841279 19.1784913 6.9123182 14.0398512 5.4306752
AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B 0.6073717 0.04975775 0.6134787 0.07298751 0.00000 0.2487687
CLASP1 13.5526799 12.35283775 14.1556083 13.76326557 13.13182 13.5469914
TSC2 32.7320500 38.17352944 27.5822399 42.17026495 29.80672 26.8834005
ERGIC2 44.7172508 32.80321746 39.3466555 39.48650557 43.39909 50.2330503
SPG20OS 0.5381304 1.09368501 0.7244898 0.59718645 0.00000 0.6256736
HLX 6.2637551 11.17865870 7.8712893 9.16736771 14.37628 16.5960244
AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B 0.07689474 0.1507720 0.09786017 0.2619113 0.1575402 0.06453105
CLASP1 13.62490813 16.9710611 13.60077467 13.8968860 13.8602742 12.22921493
TSC2 34.84509333 28.4612667 20.21958098 32.5546891 27.4615431 23.54882032
ERGIC2 42.40688611 38.2638739 47.46305203 60.9139775 49.9615901 42.44744246
SPG20OS 1.14031090 0.4979891 0.11591909 0.0000000 0.2601004 0.51261878
HLX 12.51026812 9.9915607 9.51009805 6.5911767 16.6818535 9.58529041
AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B 0.5359515 0.2541925 0.03687605 0.12318349 0.19023079 0.1071199 0.04977093
CLASP1 14.6816209 17.8194199 7.45372347 12.12126812 13.35520409 13.1915221 9.33933450
TSC2 24.6372396 26.2008531 18.57516955 24.93409328 30.55265058 23.8302414 22.53461135
ERGIC2 52.7945608 57.2316248 26.73416947 42.19559069 55.06737638 52.6069447 53.50340727
SPG20OS 1.7457787 0.2896233 0.58853070 0.07831531 0.08215546 0.6474833 0.41449171
HLX 7.6478274 16.6786706 8.02720308 11.32261966 13.50681928 10.7993960 7.80634047
AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B 0.7653514 0.5558158 0.1740532 0.15371699 0.01438479 0.00000 0.08903184
CLASP1 13.7508529 17.5996884 12.6138910 13.05946325 14.27644892 19.81262 15.48447534
TSC2 22.4547134 29.8519711 29.1289630 32.86532077 25.01968414 37.74851 39.78616320
ERGIC2 63.3812084 24.9680258 49.1526615 61.18580445 36.69324724 38.29398 41.85439024
SPG20OS 0.7472800 0.2826335 0.5753177 0.08625252 2.01164743 0.00000 0.45917070
HLX 5.8293813 14.4568159 11.9185654 8.91259009 10.87532853 12.23494 11.41288168
AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B 0.3333328 0.3947641 0.2043082 0.09667073 0.03777452 0.1960563 0.3068482
CLASP1 20.6625532 14.2786513 12.6039606 14.22788015 8.92563489 15.1424610 15.1612252
TSC2 25.4884495 25.5005665 21.6577332 34.76709325 48.83718109 26.3056873 41.6536366
ERGIC2 53.3342700 59.8592141 41.5109191 79.31730708 23.54580072 55.4573597 44.6029527
SPG20OS 0.1639835 0.2090360 0.0000000 0.60725272 0.45767049 0.0000000 2.2661783
HLX 17.4088069 12.6010172 10.0983550 6.03572098 15.45410992 10.6818107 8.5080819
AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B 0.05408842 0.1239154 0.3031964 0.1099199 0.3931737 0.3679884 0.3869206
CLASP1 14.27737042 14.6809426 16.5016818 11.2746586 7.7283789 17.8379990 13.8728423
TSC2 32.80951573 33.3896675 31.7698775 25.4769891 47.3290790 33.7824125 24.9853128
ERGIC2 40.17875502 51.1180893 57.7184021 35.0032303 16.5691962 36.2175259 54.5784482
SPG20OS 0.09993444 0.1537878 0.2822066 0.1345853 0.1377439 0.1253389 0.1199264
HLX 10.53306579 18.4490750 8.6836860 11.6405492 5.8029265 7.0288823 15.7095021
AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B 0.05036387 0.04245563 0.3515309 0.1448049 0.001221554 0.5517809 0.3788969
CLASP1 18.51104419 15.51419290 16.4582718 15.0158282 9.127337396 17.8316263 10.2478628
TSC2 30.22284533 25.01265542 32.8013656 27.5119932 20.209282551 23.1438088 45.4125204
ERGIC2 41.16504244 50.98354316 49.9366880 50.5148769 33.069097494 49.5957469 29.5490089
SPG20OS 1.28826035 0.51646543 0.8318301 1.2944474 0.073219893 0.4486587 0.2988650
HLX 10.73029358 17.32316123 14.3502361 3.7544269 9.520771392 13.0328029 8.2901708
AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B 0.58057106 0.2821525 0.08606747 0.01869908 0.25238204 0.4132298 0.01415905
CLASP1 17.68660801 14.8407452 19.55809704 19.34489523 13.31725704 9.4261484 11.19217670
TSC2 34.63917185 37.7623452 22.79335381 47.16721045 29.57293557 32.2184511 22.58957098
ERGIC2 41.38959712 48.8684912 56.08642907 52.99193057 55.65582680 32.7896973 36.60515893
SPG20OS 0.09096187 0.3101016 0.31396785 0.79112588 0.08219574 0.6836773 0.06611304
HLX 6.84981814 13.4309882 11.45157177 13.50679998 6.81095190 7.2381350 15.63307167plot(CPM[,1], countdata[,1], ylim= c(0,50), xlim= c(0,30))
abline(v= 18)
thresh<- CPM > 18
head(thresh) AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE TRUE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE TRUE FALSE FALSE FALSE
AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE FALSE TRUE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE FALSE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE TRUE FALSE FALSE FALSE FALSE FALSE
AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 TRUE FALSE FALSE FALSE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE FALSE
AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B FALSE FALSE FALSE FALSE FALSE FALSE FALSE
CLASP1 FALSE FALSE TRUE TRUE FALSE FALSE FALSE
TSC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
ERGIC2 TRUE TRUE TRUE TRUE TRUE TRUE TRUE
SPG20OS FALSE FALSE FALSE FALSE FALSE FALSE FALSE
HLX FALSE FALSE FALSE FALSE FALSE FALSE FALSEtable(rowSums(thresh))
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
11088 414 301 212 177 120 136 126 96 85 88 83 79 66 61 51 51 75
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
72 59 76 58 67 56 47 51 41 57 54 56 59 58 43 55 56 48
36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
62 48 64 43 55 56 63 50 64 61 69 68 73 72 74 99 99 122
54 55 56 57 58 59 60
116 146 184 181 251 405 2798 keep<- rowSums(thresh) >= 2
summary(keep) Mode FALSE TRUE
logical 11502 8143 y <- y[keep,keep.lib.size=FALSE]y<- calcNormFactors(y)
yAn object of class "DGEList"
$counts
AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST AI007_P62_POST
CLASP1 8.292238 6.906624 10.074986 9.082710 12.932691 8.830644 8.501854
TSC2 20.418217 20.961425 14.679039 21.802436 22.728013 17.613419 20.533438
ERGIC2 24.294538 31.684413 36.834077 33.136172 33.793841 34.650058 28.051983
HLX 6.487158 7.330773 11.580029 4.331651 8.534877 3.651586 3.929373
CP 11.511853 25.831897 6.207498 5.939641 2.835163 30.697666 0.000000
AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST AI007_P30_POST AI007_P33_POST
CLASP1 7.410743 9.211120 8.823392 8.2528837 8.537832 8.894874 11.143499
TSC2 22.901153 17.947891 27.034630 18.7324655 16.942948 22.748243 18.688171
ERGIC2 19.679383 25.603050 25.314118 27.2747882 31.658791 27.684878 25.124736
HLX 6.706327 5.121884 5.877041 9.0349844 10.459450 8.167194 6.560635
CP 4.533726 11.995819 15.971785 0.2165844 0.000000 9.457096 8.434184
AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST AI007_P2_POST
CLASP1 9.534569 9.297570 8.200424 8.39604851 9.687422 11.241436 4.810937
TSC2 14.174560 21.780383 16.247608 16.16759857 16.256470 16.528889 11.989173
ERGIC2 33.273087 40.753877 29.559750 29.14257278 34.835607 36.104748 17.255324
HLX 6.666877 4.409760 9.869810 6.58084462 5.046291 10.521791 5.181085
CP 1.926218 7.186049 5.628690 0.05368532 10.312428 9.599091 10.747973
AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
CLASP1 8.952764 9.403073 8.582158 6.313342 8.825053 11.432484 8.232963
TSC2 18.416312 21.511376 15.503511 15.233282 14.411036 19.391376 19.012188
ERGIC2 31.165647 38.771596 34.225098 36.168030 40.676933 16.218841 32.081459
HLX 8.362882 9.509822 7.025886 5.277046 3.741193 9.390923 7.779131
CP 9.636731 8.296421 7.785506 9.009380 1.378040 5.245250 12.632921
AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
CLASP1 7.893735 11.081349 12.527255 10.051809 12.04449 8.659109 8.376159
TSC2 19.865298 19.420225 23.867881 25.827346 14.85757 15.464499 14.392986
ERGIC2 36.983490 28.481219 24.212771 27.169944 31.08929 36.300871 27.586732
HLX 5.387176 8.441407 7.735992 7.408718 10.14784 7.641729 6.711020
CP 22.889810 10.502402 10.242538 20.321663 16.69494 18.587691 4.962621
AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE
CLASP1 9.354027 5.992782 9.225845 8.691569 8.5914570 8.929187 10.230658
TSC2 22.857398 32.789891 16.027263 23.879038 19.7432395 20.308136 19.696582
ERGIC2 52.146645 15.808943 33.788499 25.569811 24.1777047 31.090848 35.784062
HLX 3.968145 10.376082 6.508106 4.877481 6.3383087 11.221026 5.383683
CP 7.048288 0.000000 4.897516 20.190741 0.2995237 1.952987 6.241647
AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE
CLASP1 7.692986 4.636586 10.7233721 8.797528 11.584813 10.31492 9.728493
TSC2 17.383597 28.394745 20.3084091 15.844553 18.914439 16.63016 19.388904
ERGIC2 23.883594 9.940572 21.7722856 34.611179 25.762422 33.89742 29.517601
HLX 7.942643 3.481425 4.2254358 9.962254 6.715367 11.51765 8.482432
CP 16.296264 0.000000 0.3450054 15.404036 5.236207 5.01858 12.467803
AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE
CLASP1 9.381492 7.210589 11.036800 6.291217 11.247109 8.841927 12.240379
TSC2 17.188765 15.965317 14.324750 27.878986 22.027431 22.498326 14.265156
ERGIC2 31.560358 26.124560 30.697052 18.140293 26.320101 29.115226 35.101532
HLX 2.345667 7.521402 8.066591 5.089380 4.355875 8.002012 7.166934
CP 78.443385 12.113838 7.752517 6.637065 7.552611 3.457671 4.392075
AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
CLASP1 11.551067 8.446844 6.759687 8.825848
TSC2 28.164102 18.757464 23.104523 17.813525
ERGIC2 31.642112 35.301270 23.514175 28.865839
HLX 8.065071 4.320037 5.190617 12.327818
CP 3.008328 6.152549 2.868452 26.953178
8138 more rows ...
$samples55 more rows ...design<- model.matrix(~0+group)
colnames(design) <- levels(group)
design post.s pre.s
1 1 0
2 1 0
3 1 0
4 1 0
5 1 0
6 1 0
7 1 0
8 1 0
9 1 0
10 1 0
11 1 0
12 1 0
13 1 0
14 1 0
15 1 0
16 1 0
17 1 0
18 1 0
19 1 0
20 1 0
21 1 0
22 1 0
23 1 0
24 1 0
25 1 0
26 1 0
27 1 0
28 1 0
29 1 0
30 1 0
31 0 1
32 0 1
33 0 1
34 0 1
35 0 1
36 0 1
37 0 1
38 0 1
39 0 1
40 0 1
41 0 1
42 0 1
43 0 1
44 0 1
45 0 1
46 0 1
47 0 1
48 0 1
49 0 1
50 0 1
51 0 1
52 0 1
53 0 1
54 0 1
55 0 1
56 0 1
57 0 1
58 0 1
59 0 1
60 0 1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"par(mfrow= c(1,1))
v<- voom(y,design, plot= TRUE)
vAn object of class "EList"
$targets55 more rows ...
$E
AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST AI007_P62_POST
CLASP1 3.777680 3.499812 3.995957 3.863328 4.350648 3.779075 3.9406886
TSC2 5.028137 5.034670 4.517381 5.082024 5.140765 4.736085 5.1650792
ERGIC2 5.273400 5.619286 5.815794 5.674836 5.702849 5.692554 5.6059855
HLX 3.446155 3.580151 4.187925 2.875411 3.778476 2.610761 2.9175689
CP 4.227836 5.329735 3.339148 3.289875 2.340729 5.520465 -0.2295336
AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST AI007_P30_POST AI007_P33_POST
CLASP1 3.723906 3.920196 3.865721 3.9113302 3.8097907 3.757951 4.247978
TSC2 5.288600 4.845943 5.428042 5.0470436 4.7583859 5.065127 4.968671
ERGIC2 5.074903 5.346705 5.334955 5.5772758 5.6409552 5.342927 5.385991
HLX 3.589357 3.131612 3.317754 4.0348023 4.0879174 3.641642 3.526324
CP 3.071719 4.283932 4.686791 0.3007802 -0.3661861 3.841803 3.865861
AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST AI007_P2_POST
CLASP1 4.021887 3.866923 3.811409 3.8679597 3.910493 4.208907 3.591905
TSC2 4.570225 5.052201 4.756206 4.7737694 4.628422 4.745282 4.825545
ERGIC2 5.772782 5.940957 5.600084 5.6043939 5.704826 5.849329 5.333119
HLX 3.536324 2.870151 4.064640 3.5387165 3.033299 4.117657 3.689105
CP 1.973689 3.516741 3.305902 -0.1380667 3.996394 3.991523 4.674532
AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
CLASP1 3.948276 3.814100 3.924495 3.546996 3.843889 4.161987 3.793757
TSC2 4.949099 4.966402 4.741777 4.754381 4.521086 4.899236 4.953590
ERGIC2 5.692387 5.801638 5.859367 5.975084 5.986542 4.648568 5.693266
HLX 3.855316 3.829569 3.653321 3.308965 2.707247 3.891270 3.716766
CP 4.049061 3.643141 3.792050 4.027984 1.532005 3.107535 4.382402
AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
CLASP1 3.726037 4.138434 4.336063 3.944319 4.230665 3.725594 3.822706
TSC2 5.004765 4.920865 5.239511 5.263390 4.522562 4.527182 4.569332
ERGIC2 5.884908 5.461749 5.259787 5.335148 5.563047 5.732055 5.484587
HLX 3.214300 3.765205 3.674545 3.528344 3.994172 3.555722 3.522974
CP 5.204532 4.064449 4.057865 4.924914 4.685596 4.784957 3.122364
AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE
CLASP1 4.154996 3.4985153 3.988573 3.855114 3.9566894 3.842557 4.031387
TSC2 5.400090 5.8566907 4.753525 5.262372 5.1115462 4.984499 4.943759
ERGIC2 6.572552 4.8272698 5.806402 5.359111 5.3973142 5.586858 5.788984
HLX 3.013959 4.2427654 3.515774 3.081733 3.5458175 4.156450 3.164440
CP 3.770432 -0.2003216 3.139045 5.025716 0.4493907 1.899963 3.360821
AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE
CLASP1 3.800341 3.4019002 4.2382349 3.811574 4.243918 4.223056 3.996602
TSC2 4.926516 5.8938256 5.1288954 4.625465 4.927853 4.886572 4.955973
ERGIC2 5.373790 4.4252192 5.2269783 5.728585 5.363722 5.892334 5.549817
HLX 3.843646 3.0343751 2.9902480 3.981849 3.499867 4.375188 3.809187
CP 4.836020 0.0410904 0.5068331 4.586048 3.168891 3.252403 4.338943
AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE
CLASP1 3.883110 3.631263 4.306334 3.603371 4.172570 3.786341 4.339511
TSC2 4.723142 4.725780 4.668099 5.666452 5.111947 5.086078 4.552299
ERGIC2 5.581099 5.419107 5.741500 5.060053 5.363579 5.450888 5.822042
HLX 2.087147 3.688276 3.876884 3.322389 2.898067 3.650425 3.606824
CP 6.881127 4.341357 3.822997 3.675032 3.627793 2.547273 2.958621
AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
CLASP1 4.231314 3.771631 3.568651 4.006333
TSC2 5.481398 4.877598 5.269735 4.979936
ERGIC2 5.646618 5.772191 5.294558 5.661165
HLX 3.738690 2.879296 3.217329 4.466302
CP 2.451008 3.344159 2.460829 5.564000
8138 more rows ...
$weights
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 6.132821 6.323556 6.437323 6.375542 6.375045 6.679664 5.206287 5.409930 6.138296 6.111870 5.134229
[2,] 9.072863 9.087302 9.095672 9.091149 9.091112 9.112929 9.015002 9.028571 9.073285 9.071275 9.010048
[3,] 9.434963 9.447456 9.452282 9.450240 9.450224 9.460068 9.380118 9.394638 9.435328 9.433563 9.374337
[4,] 3.547225 3.740831 3.858917 3.794548 3.794033 4.103236 2.834106 2.991010 3.552707 3.526290 2.779316
[5,] 2.382388 2.508922 2.585942 2.543968 2.543632 2.754007 1.926546 2.023283 2.385979 2.368675 1.893061
[,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 6.179959 6.896016 5.646705 5.731130 6.562018 5.765628 5.587190 6.647784 6.033025 2.632132 5.639361
[2,] 9.076480 9.127719 9.043595 9.048770 9.104646 9.050859 9.039891 9.110701 9.066553 8.486099 9.043141
[3,] 9.438093 9.466732 9.408336 9.413053 9.456332 9.414957 9.404959 9.459063 9.429259 9.144571 9.407922
[4,] 3.594566 4.303067 3.173760 3.236299 3.990597 3.261958 3.129894 4.074121 3.462902 1.468931 3.168337
[5,] 2.413390 2.908688 2.137363 2.178452 2.671736 2.195304 2.108527 2.731585 2.327137 1.089671 2.133799
[,23] [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33]
[1,] 7.039087 5.400551 5.153176 6.248899 6.491184 5.940153 6.022378 6.363891 6.570632 7.157016 6.923006
[2,] 9.137201 9.027959 9.011358 9.081713 9.099573 9.061198 9.065944 9.090290 9.136594 9.186961 9.165332
[3,] 9.471000 9.394081 9.375867 9.442620 9.454043 9.424380 9.428705 9.449852 9.400262 9.436130 9.421066
[4,] 4.437364 2.983717 2.793686 3.664402 3.915504 3.392700 3.454831 3.782474 3.696647 4.276691 4.042820
[5,] 3.013405 2.018800 1.901630 2.459028 2.622823 2.281107 2.321847 2.536092 2.841339 3.312300 3.111432
[,34] [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44]
[1,] 7.233127 6.308359 5.046473 5.408590 6.096481 6.424026 5.601566 6.755853 6.739950 5.646449 3.737042
[2,] 9.195512 9.117424 9.033454 9.057927 9.101248 9.125993 9.070284 9.151407 9.150061 9.073149 8.915485
[3,] 9.442083 9.382198 9.283779 9.316388 9.364521 9.391210 9.330600 9.411359 9.410421 9.333821 9.172815
[4,] 4.373608 3.447620 2.514255 2.763415 3.253148 3.556333 2.900592 3.877982 3.862234 2.932826 1.850097
[5,] 3.395501 2.648695 1.956048 2.137802 2.498335 2.732780 2.237336 2.981687 2.969496 2.260671 1.480039
[,45] [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] 5.764979 6.830537 6.463298 5.488770 6.507533 6.946668 6.234744 5.558846 5.142351 6.667052 7.060982
[2,] 9.080804 9.157678 9.128860 9.063125 9.132066 9.167271 9.111874 9.067593 9.039981 9.143844 9.176533
[3,] 9.342184 9.415731 9.393658 9.322365 9.396396 9.422417 9.376132 9.327504 9.292538 9.406085 9.428869
[4,] 3.018544 3.952390 3.593641 2.820133 3.635909 4.063154 3.379340 2.870027 2.577944 3.790476 4.161968
[5,] 2.322633 3.039293 2.761642 2.179000 2.794343 3.129874 2.595895 2.215190 2.002630 2.913953 3.214137
[,56] [,57] [,58] [,59] [,60]
[1,] 6.337697 6.519827 6.722476 6.080606 5.509847
[2,] 9.119615 9.132952 9.148578 9.100300 9.064476
[3,] 9.384592 9.397153 9.409387 9.363485 9.323919
[4,] 3.475028 3.647702 3.844969 3.242165 2.835108
[5,] 2.669892 2.803467 2.956131 2.489845 2.189867
8138 more rows ...
$design
[,1] [,2]
1 1 0
2 1 0
3 1 0
4 1 0
5 1 0
55 more rows ...fit<- lmFit(v)
names(fit) [1] "coefficients" "stdev.unscaled" "sigma" "df.residual" "cov.coefficients"
[6] "pivot" "rank" "Amean" "method" "design" Coding error is still being resolved
cont.matrix<- makeContrasts(PRE.svPOST.s= pre.s - post.s, levels= design)Error in makeContrasts(PRE.svPOST.s = pre.s - post.s, levels = design) :
The levels must by syntactically valid names in R, see help(make.names). Non-valid names: post.s, pre.sAlmost to volcano plot figure however, some coding issues are still being resolved
Multiple sequence analysis and Pathway analysis
ESR1SequenceFile<- system.file("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1Sequences<- readAAStringSet("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1SequencesAAStringSet object of length 3:
width seq names
[1] 6327 AGCTGGCGGAGGGCGTTCGTCCTGGGACTGCACTTGCTC...CTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2] 7949 TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTAT...CTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3] 2438 GTATTTTTCAGAATATCCTTTCTAGGTACAGTTTTTCAG...ATCACGGGGGACGCAGAGGGTTTCCCCGCCACAGTCTGA XM_015137107.2 PR...FirstAlignment<- msa(ESR1Sequences)use default substitution matrixFirstAlignmentCLUSTAL 2.1
Call:
msa(ESR1Sequences)
MsaAAMultipleAlignment with 3 rows and 8024 columns
aln names
[1] ------------------------------------------...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2] TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTATAAC...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3] ------------------------------------------...----------------------------------------- XM_015137107.2 PR...
Con ------------------------------------------...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA Consensus print(FirstAlignment, show= "complete")
MsaAAMultipleAlignment with 3 rows and 8024 columns
aln (1..86) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTATAACCTTCAGTTCAGAATTCATTAGCTGTCCTATTTTGAGAACTGTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (87..172) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] CTCTATGTAATTTTCGTCTCTGTATTGATGTGTAAAACTGGTTTTAACAGGTAGCTAAATGCTGTTTGAAAAGCATACTTCACCCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (173..258) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TTCTGGCAACTAAAATAATTGAAAGATTTAATTAATTTAGAAAAAATATTTCACTTTCAAAACACTTAAACTGTTCAGAGCATGTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (259..344) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] ATTCAATAATCTACCTTTCACCAGAAATCATAATAAACACAATAAAAATGCTTACAGAACCCCCACAATGCGTTAGTATACACGAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (345..430) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TATTCCTTGTGTAAGTGAATCTTGTTGAGATTTTATGTTCAGTCAATTGAAATTAAATACTTTACATATTAACTAAAATGTGTCCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (431..516) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] GCTCTATGTATTCTGGAGAAGTTACTCTCAGACAAATTTACATATTTAAATTATTTTATGGGCTAACTGATAAGTATAGAGAAGAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (517..602) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TGAAGACAGTTAAGATCATTTATTTCAAAATGTTTTAAAGTGTTGATTATTTATTTTGGTTTTCTTTCTTTCCCATGCCAGTTTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (603..688) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AGATGCACCTCTTACTTGGCAGCTGTTCCTCTGTACTGGGTACTGGGACAGAGAGAAATACAGTAGCAAGAGGGAGATCCTGCCTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (689..774) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] CGCCCCATTCTACCATTCTCACTGCCAGAAAGCCAGCCTTTTTTCAAGGCTTGTAGAGAAGAAAATGCGAAAATATTTTTAAAAAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (775..860) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TCATTTAAAGTACCTACTGCATAAACCACACCAGACATGATGAGATATTAAAATGTCAATATTATTAAAAATTTTTAATATGATTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (861..946) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TACAGCCCCTTTGCTACTTTAAAATGTTTATCTTAGTGTTAAACAAACAATCAATAACCTCATAAACTTAAAAATTGCTGCAGGAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (947..1032) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] ATACCGGACAGTTTATGGAAGGATCATATGACAGAAGGAAGGGCTGAAGAGTGTGAGAAGCTAGACCTCTGCAGGTTACCGAAGTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (1033..1118) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AAGAACCTCATTAATCAGTAACAAGAAGTGCAGAGCGGGCTTTTGAGTCCATGCCTGAGTAAGAAAGTCCCAAAAAACACTCACAG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus
aln (1119..1204) names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AAGATATTTCCTTGCCCCTGCTTTTAGTTTAGCTGTAGCTAACTTTGGATTAACAAAATTTATGTGCTGAATGATGTTTTATTTTT XM_009452243.3 PR...
[3] ------GTATTTTTCAGAATATCCTTTCTAGGTACAGTTTTTCAGTTCTAGTGCACAGAATGGAAACTTGTTACCTGCTATACCAC XM_015137107.2 PR...
Con ------?T???TT?C??????T??T???T??G???????T??C??T???????CA?A???T?????CT???T??????T??????? Consensus
aln (1205..1290) names
[1] -----------------------------------------------------------AGCTG---------------------- NM_000125.4 Homo ...
[2] TTTTCCAACTCCACATGCCTGTCTAGACTTCAAGCTTTATTATGAATAAAGAGAAAATCGGCTGGATGGCATAAAAAATATTTCAG XM_009452243.3 PR...
[3] ATTTTCACTAGGATGTGATGTATTTATCACAAACAACAGTATTGGTCAACATTTTCCCTCGCTGTGAAGTGCACATTTGACATCCT XM_015137107.2 PR...
Con ?TTT?CA?????A??TG??????T???C???AA??????T??TG???AA???????????GCTG????G???A?A????A??TC?? Consensus
aln (1291..1376) names
[1] -----------------------------------------------------------------------GCGGAGGGCGTTCGT NM_000125.4 Homo ...
[2] GCAGATTAACACATGATT--------------------TACCTCTTCTTGAACATCCATCTTAATGGAAGTGCTAAGAAAGTTAGA XM_009452243.3 PR...
[3] TTAGAAAAATTACTGACGGTTTTGAGACGATTGTTTTGTGCTTTCTTTCAGTCAACGTAATTTTCCCGAAAGCAGAGATGACTCTT XM_015137107.2 PR...
Con ??AGA??AA????TGA??--------------------T?C?T??T?T????CA?C????TT??????A??GC?GAGA??GTTCGT Consensus
aln (1377..1462) names
[1] CCTGG------------GACTG------------------CACTTGCTCC------------------------------------ NM_000125.4 Homo ...
[2] TTCGG------------GCCTGGCTTGGCAAAAGCAAGGCCACCCCCTCCTCTATTTTTTCAATGAGATTTTCCAATCCTAGTCAA XM_009452243.3 PR...
[3] CCAGACATGCTAACAATGCCTG-----AACAAACTGTGTAAGCTTAGTCCAAAAAAAATATTTG---------------------- XM_015137107.2 PR...
Con CC?GG------------GCCTG-----???AAA????G??CACTT?CTCC???A????T?????---------------------- Consensus
aln (1463..1548) names
[1] -------------------------------------------------------------CGTCGGG-------TCGCCCGGCTT NM_000125.4 Homo ...
[2] ATGGTGGTGCTAGTTCTTTATTTTTGAGTTACTGCATTTCCTAATTTCATGGTCGTAACAGCCTCCTG-------TCTACCGACTC XM_009452243.3 PR...
[3] ---------------------ATTAATAGATTTTATTTTGGTAGATTCTAAGGTTCTAAGCAGTCAGAGAAATAATCGCAGAGCCT XM_015137107.2 PR...
Con ---------------------?TT????????T???TTT??TA??TTC???G?????A???CGTC?GG-------TCGCCCGGCTT Consensus
aln (1549..1634) names
[1] C--------------------ACCGGACCCGCAG--------------------GCTCCCGGGGCAGGG---------CCGGGGC- NM_000125.4 Homo ...
[2] AGAACGGATTTTACCAAA---ACTGAAAATGCAG--------------------GCTCCATGCTCAGAAGCTCTTTAACAGGCTC- XM_009452243.3 PR...
[3] CAAATATCTCCAAAATCTGATACCAATCCCTTTGATTGTGAATTATATTCTGTAGCTACCAAAGAAGGGAGAAGAAAACTAGGAAG XM_015137107.2 PR...
Con C?AA????T???A?????---ACCGAACCCGCAG--------------------GCTCCC?G?GCAGGG???????AAC?GGG?C- Consensus
aln (1635..1720) names
[1] ---------CAGAG-----CTCGCGTGTCGGCGGGACATGCGCTG-----------------------------CGTCGCCTCTA- NM_000125.4 Homo ...
[2] ---------GAAAGGTCCATGCTCCTTTCTCCTGCCCATTCTATAGCATAAGAAGACAGTCTCTGAGTGATAATCTTCTCTTCAAG XM_009452243.3 PR...
[3] GAGTAAGCACAAAGATCTCTTCACGT-TCTCCGGAACTGTAGTAGCAAATAGCAG-----------------CACGGCGCTTCTTG XM_015137107.2 PR...
Con ---------CAAAG?TC??TTC?CGT?TCTCCGG?ACATTCG?TG??A??AG?AG-----------------??CGTCGCTTCTAG Consensus
aln (1721..1806) names
[1] --------------------------ACCTCGGGCTGTGCTCTTTTTCCAG----------------------------------- NM_000125.4 Homo ...
[2] AAGAAGAAAACTAGGAAGGAGTAAGCACAAAGATCTCTTCACATTCTCTGGGACTGCGGTACCAAATATCAGCACAGCACTTCTTG XM_009452243.3 PR...
[3] AAAAAGG---------------ATGTAGATTTTAATCTGAACTTTGAACCG----------------------------------- XM_015137107.2 PR...
Con AA?AAG?---------------A?G?ACAT?G??CTCTGCACTTT?TCC?G----------------------------------- Consensus
aln (1807..1892) names
[1] --------------------------------------------GTGGCCCGCCGGTTTCTGAGCCTTCTGCCCTGCGGGGACACG NM_000125.4 Homo ...
[2] AAAAAGGATGTAGATTTTAATCTGAACTTTGAACCATCACTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG XM_009452243.3 PR...
[3] ------------------------------------TCATTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG XM_015137107.2 PR...
Con ------------------------------------TCA?TGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG Consensus
aln (1893..1978) names
[1] GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCTGGGATGGCCCTACTGCATCAGATCCAAG NM_000125.4 Homo ...
[2] GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG XM_009452243.3 PR...
[3] GTCTGCGCCCTGCCCACGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG XM_015137107.2 PR...
Con GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG Consensus
aln (1979..2064) names
[1] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACCTGGACAGCAGCAAG NM_000125.4 Homo ...
[2] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG XM_009452243.3 PR...
[3] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG XM_015137107.2 PR...
Con GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG Consensus
aln (2065..2150) names
[1] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGG NM_000125.4 Homo ...
[2] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCGGCCAACGCGCAGGTCTACGGTCAGACCGG XM_009452243.3 PR...
[3] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGCCAGACTGG XM_015137107.2 PR...
Con CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGG Consensus
aln (2151..2236) names
[1] CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA NM_000125.4 Homo ...
[2] CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTCGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA XM_009452243.3 PR...
[3] CCTCCCGTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA XM_015137107.2 PR...
Con CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA Consensus
aln (2237..2322) names
[1] GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC NM_000125.4 Homo ...
[2] GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_009452243.3 PR...
[3] GCCCGCTGATGCTGCTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_015137107.2 PR...
Con GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC Consensus
aln (2323..2408) names
[1] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA NM_000125.4 Homo ...
[2] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA XM_009452243.3 PR...
[3] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCTCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA XM_015137107.2 PR...
Con GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA Consensus
aln (2409..2494) names
[1] AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG NM_000125.4 Homo ...
[2] AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG XM_009452243.3 PR...
[3] GAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG XM_015137107.2 PR...
Con AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG Consensus
aln (2495..2580) names
[1] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAG------GACATAACGAC NM_000125.4 Homo ...
[2] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC XM_009452243.3 PR...
[3] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC XM_015137107.2 PR...
Con CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC Consensus
aln (2581..2666) names
[1] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGTAAATGCTACGA NM_000125.4 Homo ...
[2] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA XM_009452243.3 PR...
[3] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAGAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA XM_015137107.2 PR...
Con TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA Consensus
aln (2667..2752) names
[1] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG NM_000125.4 Homo ...
[2] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG XM_009452243.3 PR...
[3] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG XM_015137107.2 PR...
Con AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG Consensus
aln (2753..2838) names
[1] GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACGCTCTAAGAAGAAC NM_000125.4 Homo ...
[2] GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACACTCTAAGAAGAAC XM_009452243.3 PR...
[3] GCAGGGGTGAAGTGGGGTCCGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAGCACTCTAAGAAGAAC XM_015137107.2 PR...
Con GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACACTCTAAGAAGAAC Consensus
aln (2839..2924) names
[1] AGCCTGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCGATACTCTATTCCGAGTATGATCC NM_000125.4 Homo ...
[2] AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCCATACTCTATTCCGAGTATGATCC XM_009452243.3 PR...
[3] AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGCTGGATGCTGAGCCCCCTATACTCTATTCCGAGTATGATCC XM_015137107.2 PR...
Con AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCC?ATACTCTATTCCGAGTATGATCC Consensus
aln (2925..3010) names
[1] TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCGA NM_000125.4 Homo ...
[2] TACCAGACCCTTCAGTGAGGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA XM_009452243.3 PR...
[3] TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA XM_015137107.2 PR...
Con TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA Consensus
aln (3011..3096) names
[1] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT NM_000125.4 Homo ...
[2] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT XM_009452243.3 PR...
[3] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT XM_015137107.2 PR...
Con AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT Consensus
aln (3097..3182) names
[1] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTACTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA NM_000125.4 Homo ...
[2] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA XM_009452243.3 PR...
[3] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA XM_015137107.2 PR...
Con CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA Consensus
aln (3183..3268) names
[1] GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC NM_000125.4 Homo ...
[2] GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC XM_009452243.3 PR...
[3] GGGCATGGTGGAGATCTTCGACATGTTACTGGCCACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC XM_015137107.2 PR...
Con GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC Consensus
aln (3269..3354) names
[1] TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC NM_000125.4 Homo ...
[2] TCAAGTCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC XM_009452243.3 PR...
[3] TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC XM_015137107.2 PR...
Con TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC Consensus
aln (3355..3440) names
[1] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCAGCGGCTGGC NM_000125.4 Homo ...
[2] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC XM_009452243.3 PR...
[3] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC XM_015137107.2 PR...
Con CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC Consensus
aln (3441..3526) names
[1] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG NM_000125.4 Homo ...
[2] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG XM_009452243.3 PR...
[3] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAATGTGG XM_015137107.2 PR...
Con CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG Consensus
aln (3527..3612) names
[1] TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCATCCGTGGAGGAG NM_000125.4 Homo ...
[2] TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAG XM_009452243.3 PR...
[3] TGCCCCTCTACGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCATGGAGGAG XM_015137107.2 PR...
Con TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAG Consensus
aln (3613..3698) names
[1] ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT NM_000125.4 Homo ...
[2] ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT XM_009452243.3 PR...
[3] ACGGACCAAAGCCACTTGGCCACCGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGACGCAGAGGGTTT XM_015137107.2 PR...
Con ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT Consensus
aln (3699..3784) names
[1] CCCTGCCACGGTCTGAGAGCTCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC NM_000125.4 Homo ...
[2] CCCTGCCACAGTCTGAGAGTTCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC XM_009452243.3 PR...
[3] CCCCGCCACAGTCTGA---------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCTGCCACAGTCTGAGAG?TCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC Consensus
aln (3785..3870) names
[1] CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT NM_000125.4 Homo ...
[2] CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT Consensus
aln (3871..3956) names
[1] CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG NM_000125.4 Homo ...
[2] CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG Consensus
aln (3957..4042) names
[1] CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA NM_000125.4 Homo ...
[2] CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA Consensus
aln (4043..4128) names
[1] AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC NM_000125.4 Homo ...
[2] AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC Consensus
aln (4129..4214) names
[1] AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG NM_000125.4 Homo ...
[2] AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG Consensus
aln (4215..4300) names
[1] CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC NM_000125.4 Homo ...
[2] CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC Consensus
aln (4301..4386) names
[1] TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAGATTCAGATGTG NM_000125.4 Homo ...
[2] TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAGCTTCAGATGTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAG?TTCAGATGTG Consensus
aln (4387..4472) names
[1] CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT NM_000125.4 Homo ...
[2] CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT Consensus
aln (4473..4558) names
[1] TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT NM_000125.4 Homo ...
[2] TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT Consensus
aln (4559..4644) names
[1] TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC NM_000125.4 Homo ...
[2] TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC Consensus
aln (4645..4730) names
[1] TGTTCACTGTGGTGATGCATGATGAGGGTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATTTAGCCCTGGGGCATGGA NM_000125.4 Homo ...
[2] TGTTCACTGTGGTGATGCATGATGAGAGTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATTGAGCCCTGGGGCATGGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTCACTGTGGTGATGCATGATGAG?GTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATT?AGCCCTGGGGCATGGA Consensus
aln (4731..4816) names
[1] GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC NM_000125.4 Homo ...
[2] GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC Consensus
aln (4817..4902) names
[1] AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG NM_000125.4 Homo ...
[2] AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG Consensus
aln (4903..4988) names
[1] CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA NM_000125.4 Homo ...
[2] CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA Consensus
aln (4989..5074) names
[1] CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG NM_000125.4 Homo ...
[2] CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG Consensus
aln (5075..5160) names
[1] CCTGGTCAGATTACGTATGCCCTTGGTGGTTTAGAGATAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT NM_000125.4 Homo ...
[2] CCTGGTCAGATTACCTATGCCCTTGGTGGTTTAGAGCTAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCTGGTCAGATTAC?TATGCCCTTGGTGGTTTAGAG?TAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT Consensus
aln (5161..5246) names
[1] CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC NM_000125.4 Homo ...
[2] CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC Consensus
aln (5247..5332) names
[1] ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG NM_000125.4 Homo ...
[2] ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG Consensus
aln (5333..5418) names
[1] TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC NM_000125.4 Homo ...
[2] TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC Consensus
aln (5419..5504) names
[1] TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAGTGGATTTCATTCATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT NM_000125.4 Homo ...
[2] TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAGGGGATTTCATTAATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAG?GGATTTCATT?ATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT Consensus
aln (5505..5590) names
[1] GAGAATCTGGGAGGGCAAAAAAAAAAAAAAAGTTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT NM_000125.4 Homo ...
[2] GAGAATCTGGGAGGGCAAAAAAAAAAAAAAG-TTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GAGAATCTGGGAGGGCAAAAAAAAAAAAAA?-TTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT Consensus
aln (5591..5676) names
[1] GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT NM_000125.4 Homo ...
[2] GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT Consensus
aln (5677..5762) names
[1] TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA NM_000125.4 Homo ...
[2] TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA Consensus
aln (5763..5848) names
[1] AACCAAGGAAAAATATTTAGTTTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA NM_000125.4 Homo ...
[2] AACCAAGGAAAAATATTTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCAAGGAAAAATATTTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA Consensus
aln (5849..5934) names
[1] GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC NM_000125.4 Homo ...
[2] GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC Consensus
aln (5935..6020) names
[1] CTATTGTTGGATACTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC NM_000125.4 Homo ...
[2] CTATTGTTGGATATTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTATTGTTGGATA?TGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC Consensus
aln (6021..6106) names
[1] TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT NM_000125.4 Homo ...
[2] TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT Consensus
aln (6107..6192) names
[1] TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG NM_000125.4 Homo ...
[2] TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG Consensus
aln (6193..6278) names
[1] GTTTTACATTATTCATCCAATGTGTTTCTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA NM_000125.4 Homo ...
[2] GTTTTACATTATTCATCCAATGTGTTTGTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GTTTTACATTATTCATCCAATGTGTTT?TATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA Consensus
aln (6279..6364) names
[1] TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG NM_000125.4 Homo ...
[2] TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG Consensus
aln (6365..6450) names
[1] CTGATGTTGGTATTGGGTGTAGGAACATGATTTAAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAATGTA NM_000125.4 Homo ...
[2] CTGATGTTGGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAATTTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTGATGTTGGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAAT?TA Consensus
aln (6451..6536) names
[1] AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAAGTGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA NM_000125.4 Homo ...
[2] AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAAATGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAA?TGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA Consensus
aln (6537..6622) names
[1] TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA NM_000125.4 Homo ...
[2] TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA Consensus
aln (6623..6708) names
[1] ACTAGCTCCATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATG--GAA NM_000125.4 Homo ...
[2] ACTAGCTGCATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATGGAGAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con ACTAGCT?CATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATG--GAA Consensus
aln (6709..6794) names
[1] TAGCTAGTGGTCTGTGTTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCTATAATGCCATCATGCAGCAATTATGAGAGGCT NM_000125.4 Homo ...
[2] TAGCTAGTGGTCTGTATTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCTGTAATGCCATCATGCAGCAATTATGAGAGGCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TAGCTAGTGGTCTGT?TTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCT?TAATGCCATCATGCAGCAATTATGAGAGGCT Consensus
aln (6795..6880) names
[1] AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT NM_000125.4 Homo ...
[2] AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT Consensus
aln (6881..6966) names
[1] AACCTTGCAGATATGTTTAACCAAGCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA NM_000125.4 Homo ...
[2] AACCTTGCAGATATGTTTAACCACGCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCTTGCAGATATGTTTAACCA?GCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA Consensus
aln (6967..7052) names
[1] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCACTGGCTTAGAGTACTCCTTCCCCTG NM_000125.4 Homo ...
[2] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCATTGGCTTAGAGTACTCCTTCCCCTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCA?TGGCTTAGAGTACTCCTTCCCCTG Consensus
aln (7053..7138) names
[1] CATGACACTGATTACAAATACTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAGTGATCACTAACACCAT NM_000125.4 Homo ...
[2] CATGACACTGATTACAAATCCTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAATGATCACTAACACCAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CATGACACTGATTACAAAT?CTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGA?TGATCACTAACACCAT Consensus
aln (7139..7224) names
[1] AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC NM_000125.4 Homo ...
[2] AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC Consensus
aln (7225..7310) names
[1] AACCATAATTCTCTTTGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT NM_000125.4 Homo ...
[2] AACCATAATTCTCTTCGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCATAATTCTCTT?GGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT Consensus
aln (7311..7396) names
[1] CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT NM_000125.4 Homo ...
[2] CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT Consensus
aln (7397..7482) names
[1] CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT NM_000125.4 Homo ...
[2] CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT Consensus
aln (7483..7568) names
[1] TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG NM_000125.4 Homo ...
[2] TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG Consensus
aln (7569..7654) names
[1] CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA NM_000125.4 Homo ...
[2] CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA Consensus
aln (7655..7740) names
[1] CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA NM_000125.4 Homo ...
[2] CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA Consensus
aln (7741..7826) names
[1] CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATTG NM_000125.4 Homo ...
[2] CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATCG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAAT?G Consensus
aln (7827..7912) names
[1] TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA NM_000125.4 Homo ...
[2] TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA Consensus
aln (7913..7998) names
[1] AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG NM_000125.4 Homo ...
[2] AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG Consensus
aln (7999..8024) names
[1] ATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2] ATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3] -------------------------- XM_015137107.2 PR...
Con ATGTTCAAATAAAGAATTAAACTAAA Consensus Pathway Analysis Since Pathway analysis directly connects to the results of RNA-seq, once the previous coding error unde the RNA-seq data is worked out, pathway analysis will be shown, for now, below is a comment of the skeleton of the input
#go<- goana(tr, species= "Homo Sapien")
#topGO(go, n=15)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